Genetic and epigenetic fine mapping of causal autoimmune disease variants
Mikhail Dozmorov
November 1, 2014
Genetic and epigenetic fine mapping of causal autoimmune disease variants
Supplemental table 1 has genomic coordinates of disease-associated SNPs.
Analysis of TFBSs
Out of all regulatory datasets, we select only TFBSs.
## [1] 1954 39## [1] 1259 38
Text mining question 1: Are the diseases within a cluster share stronger literature similarity than the diseases between the clusters? To answer, we need literature similarity scores for each pair, then split the pairs into cluster-specific groups and compare score distributions with what can be expected by chance, calculating the p-values for it. Expected answer: Diseases within each cluster are related to each other by literature findings stronger than could be expected by chance. Diseases between the clusters are not related to each other by literature findings, and this also may be statistically significant.
The top 10 pairs of disease-associated SNPs are most similar with each other.
##
## -----------------------------------------------------------------------------------------------
## Disease 1 Disease 2 Corr. coefficient
## ---------------------------------------------- ---------------------------- -------------------
## HDL_cholesterol Triglycerides 0.5484
##
## Kawasaki_disease Systemic_lupus_erythematosus 0.5352
##
## Bone_mineral_density Type_2_diabetes 0.5268
##
## Kawasaki_disease Multiple_sclerosis 0.501
##
## Kawasaki_disease Rheumatoid_arthritis 0.4775
##
## Celiac_disease Kawasaki_disease 0.4754
##
## LDL_cholesterol Triglycerides 0.4743
##
## Kawasaki_disease Ulcerative_colitis 0.4661
##
## Liver_enzyme_levels_gamma_glutamyl_transferase Urate_levels 0.4191
##
## Alzheimers_combined Bone_mineral_density 0.4149
## -----------------------------------------------------------------------------------------------The similarity dendrogram can be divided into separate groups:
## Cluster01 has 8 members
## Kawasaki_disease
## Systemic_lupus_erythematosus
## Celiac_disease
## Ulcerative_colitis
## Psoriasis
## Multiple_sclerosis
## Rheumatoid_arthritis
## Allergy
##
## Cluster02 has 12 members
## Systemic_sclerosis
## Primary_biliary_cirrhosis
## Atopic_dermatitis
## Juvenile_idiopathic_arthritis
## Ankylosing_spondylitis
## Crohns_disease
## Type_1_diabetes
## Primary_sclerosing_cholangitis
## Creatinine_levels
## Behcets_disease
## Progressive_supranuclear_palsy
## Restless_legs_syndrome
##
## Cluster03 has 18 members
## Vitiligo
## Migraine
## Alopecia_areata
## Asthma
## Chronic_kidney_disease
## Alzheimers_combined
## Bone_mineral_density
## Type_2_diabetes
## Urate_levels
## Liver_enzyme_levels_gamma_glutamyl_transferase
## LDL_cholesterol
## HDL_cholesterol
## Triglycerides
## Renal_function_related_traits_BUN
## Platelet_counts
## Red_blood_cell_traits
## C_reactive_protein
## Fasting_glucose_related_traits
## The “Enrichment 1/2” columns show the average p-values of the group-specific SNPs-regulatory associations. A “-” sign indicates that an association is underrepresented. The “p-value” column shows whether the difference in the associations between the groups is statistically significantly different.
## [1] "c1 vs. c2 , number of degs significant at adj.p.val<0.5: 164"
##
## -------------------------------------------------------------------------------------------------------
## Row.names V2 c1 c2 adj.P.Val
## --------------------------------------------- ----------------------------- ------- ------- -----------
## wgEncodeUwTfbsGm12864CtcfStdHotspotsRep1 GM12864 CTCF TFBS ChIP-seq 0.8086 0.9994 1
## Hotspots 1 from ENCODE/UW
##
## wgEncodeHaibTfbsSknshMef2aV0422111PkRep1 SK-N-SH MEF2A v042211.1 0.5821 0.8092 1
## ChIP-seq Peaks Rep 1 from
## ENCODE/HAIB
##
## wgEncodeUwTfbsAg04449CtcfStdPkRep1 AG04449 CTCF TFBS ChIP-seq 0.9784 0.7917 1
## Peaks 1 from ENCODE/UW
##
## wgEncodeHaibTfbsEcc1Creb1sc240V0422111PkRep1 ECC-1 CREB1 v042211.1 0.6763 0.977 1
## ChIP-seq Peaks Rep 1 from
## ENCODE/HAIB
##
## wgEncodeSydhTfbsK562Smc3ab9263IggrabPk K562 SMC3 IgG-rab ChIP-seq 0.7659 -0.9973 1
## Peaks from ENCODE/SYDH
##
## wgEncodeAwgTfbsHaibH1hescSin3ak20Pcr1xUniPk H1-hESC TFBS Uniform Peaks of 0.7776 1 1
## Sin3Ak-20 from
## ENCODE/HudsonAlpha/Analysis
##
## wgEncodeHaibTfbsEcc1Nficsc81335V0422111PkRep1 ECC-1 NFIC v042211.1 ChIP-seq -0.7953 -0.9692 1
## Peaks Rep 1 from ENCODE/HAIB
##
## wgEncodeAwgTfbsSydhMcf10aesPol2TamUniPk MCF10A-Er-Src (TAM 36h) TFBS 0.8087 0.4704 1
## Uniform Peaks of Pol2
## ENCODE/Harvard/Analysis
##
## wgEncodeSydhTfbsMcf7Znf217UcdPk MCF-7 ZNF217 UC Davis 0.8376 0.624 1
## ChIP-seq Peaks from
## ENCODE/SYDH
##
## wgEncodeAwgTfbsHaibH1hescPol2V0416102UniPk H1-hESC TFBS Uniform Peaks of 0.9852 0.6661 1
## Pol2 from
## ENCODE/HudsonAlpha/Analysis
## -------------------------------------------------------------------------------------------------------
##
## [1] "c1 vs. c3 , number of degs significant at adj.p.val<0.5: 205"
##
## --------------------------------------------------------------------------------------------------------
## Row.names V2 c1 c3 adj.P.Val
## ----------------------------------------------- ----------------------------- ------- ------ -----------
## wgEncodeHaibTfbsK562Nr2f2sc271940V0422111PkRep1 K562 NR2F2 v042211.1 ChIP-seq 0.684 0.6837 0.9998
## Peaks Rep 1 from ENCODE/HAIB
##
## wgEncodeSydhTfbsMcf7Znf217UcdPk MCF-7 ZNF217 UC Davis 0.8376 0.8376 0.9998
## ChIP-seq Peaks from
## ENCODE/SYDH
##
## wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111PkRep2 MCF-7 HDAC2 v042211.1 0.8612 0.8965 0.9994
## ChIP-seq Peaks Rep 2 from
## ENCODE/HAIB
##
## wgEncodeHaibTfbsMcf7Gata3V0422111PkRep1 MCF-7 GATA3 v042211.1 -0.9668 -0.969 0.9982
## ChIP-seq Peaks Rep 1 from
## ENCODE/HAIB
##
## wgEncodeSydhTfbsK562Mazab85725IggrabPk K562 MAZ IgG-rab ChIP-seq 0.7785 0.7805 0.9982
## Peaks from ENCODE/SYDH
##
## wgEncodeAwgTfbsHaibH1hescSp2V0422111UniPk H1-hESC TFBS Uniform Peaks of 0.9648 0.967 0.9982
## SP2_(SC-643) from
## ENCODE/HudsonAlpha/Analysis
##
## wgEncodeUchicagoTfbsK562EfosControlPk K562 FOS GFP-tag TFBS Peaks 0.5165 0.5127 0.9976
## from ENCODE/UChicago
##
## wgEncodeHaibTfbsA549Zbtb33V0422111Etoh02PkRep1 A549 ZBTB33 EtOH v042211.1 0.8736 0.8753 0.9976
## ChIP-seq Peaks Rep 1 from
## ENCODE/HAIB
##
## wgEncodeHaibTfbsSknshGabpV0422111PkRep1 SK-N-SH GABP v042211.1 0.786 0.7822 0.9973
## ChIP-seq Peaks Rep 1 from
## ENCODE/HAIB
##
## wgEncodeSydhTfbsHelas3Rad21IggrabPk HeLa-S3 Rad21 IgG-rab 0.8496 0.8539 0.9973
## ChIP-seq Peaks from
## ENCODE/SYDH
## --------------------------------------------------------------------------------------------------------
##
## [1] "c2 vs. c3 , number of degs significant at adj.p.val<0.5: 0"
##
## ----------------------------------------------------------------------------------------------------
## Row.names V2 c2 c3 adj.P.Val
## ------------------------------------------ ----------------------------- ------- ------- -----------
## wgEncodeHaibTfbsHepg2Zbtb33Pcr1xPkRep1 HepG2 ZBTB33 PCR1x ChIP-seq 1 1 1
## Peaks Rep 1 from ENCODE/HAIB
##
## wgEncodeAwgTfbsUtaK562Pol2UniPk K562 TFBS Uniform Peaks of 0.6746 0.675 0.9996
## Pol2 from
## ENCODE/UT-A/Analysis
##
## wgEncodeAwgTfbsHaibH1hescEgr1V0416102UniPk H1-hESC TFBS Uniform Peaks of 0.9675 0.967 0.9993
## Egr-1 from
## ENCODE/HudsonAlpha/Analysis
##
## wgEncodeSydhTfbsImr90CebpbIggrabPk IMR90 CEBPB IgG-rab ChIP-seq -0.9889 -0.9869 0.9986
## Peaks from ENCODE/SYDH
##
## wgEncodeHaibTfbsPanc1NrsfPcr2xPkRep1 PANC-1 NRSF PCR2x ChIP-seq 0.8001 0.8016 0.998
## Peaks Rep 1 from ENCODE/HAIB
##
## wgEncodeSydhTfbsHelas3Stat1Ifng30StdPk HeLa-S3 STAT1 Standard IFNg 0.947 0.9509 0.9971
## 30min ChIP-seq Peaks from
## ENCODE/SYDH
##
## wgEncodeAwgTfbsSydhGm12878JundUniPk GM12878 TFBS Uniform Peaks of 0.9279 0.93 0.9959
## JunD from
## ENCODE/Yale/Analysis
##
## wgEncodeHaibTfbsK562Usf1V0416101PkRep1 K562 USF-1 v041610.1 ChIP-seq 0.7685 0.7714 0.9944
## Peaks Rep 1 from ENCODE/HAIB
##
## wgEncodeAwgTfbsSydhHct116Tcf7l2UcdUniPk HCT-116 TFBS Uniform Peaks of 0.9531 0.9489 0.9944
## TCF7L2 from
## ENCODE/USC/Analysis
##
## wgEncodeSydhTfbsGm18526NfkbTnfaIggrabPk GM18526 NFKB IgG-rab TNFa 0.9893 0.9817 0.9936
## ChIP-seq Peaks from
## ENCODE/SYDH
## ----------------------------------------------------------------------------------------------------Text mining question 2: Are the terms associated stronger with the diseases in one vs. the other cluster based on the literature strength? Are the terms themselves related based on the literature? Expected answer: Yes, the literature associations should confirm the relationships.
Summary
- There are 4 clusters. The first cluster drives all the differences.
| C1 | C2 | C3 | C4 | |
|---|---|---|---|---|
| C1 | Cell types: Gm12878 Reg: NFkB, Pol2, MTA3, NFIC, NFATC1 | Cell types: Gm12878 Reg: NFkB, Pol2, MTA3, NFIC, NFATC1 | Cell types: Gm12878 Reg: NFkB, Pol2, MTA3, NFIC, NFATC1 | |
| C2 | Nothing significant | Nothing significant | ||
| C3 | Nothing significant | |||
| C4 |
Analysis of histone marks
Out of all regulatory datasets, we select only histone marks
## [1] 721 39## [1] 610 39
Text mining question 1: Are the diseases within a cluster share stronger literature similarity than the diseases between the clusters? To answer, we need literature similarity scores for each pair, then split the pairs into cluster-specific groups and compare score distributions with what can be expected by chance, calculating the p-values for it. Expected answer: Diseases within each cluster are related to each other by literature findings stronger than could be expected by chance. Diseases between the clusters are not related to each other by literature findings, and this also may be statistically significant.
The top 10 pairs of autoimmune-associated SNPs are most similar with each other.
##
## ---------------------------------------------------------------------------------------
## Disease 1 Disease 2 Corr. coefficient
## --------------------------------- --------------------------------- -------------------
## HDL_cholesterol Triglycerides 0.621
##
## Rheumatoid_arthritis Ulcerative_colitis 0.4856
##
## HDL_cholesterol LDL_cholesterol 0.48
##
## HDL_cholesterol Platelet_counts 0.4609
##
## Platelet_counts Triglycerides 0.4504
##
## LDL_cholesterol Triglycerides 0.4151
##
## Creatinine_levels Renal_function_related_traits_BUN 0.3915
##
## Psoriasis Systemic_lupus_erythematosus 0.3911
##
## Renal_function_related_traits_BUN Urate_levels 0.3689
##
## Alopecia_areata C_reactive_protein 0.3686
## ---------------------------------------------------------------------------------------The similarity dendrogram can be divided into separate groups:
## Cluster01 has 6 members
## Celiac_disease
## Multiple_sclerosis
## Kawasaki_disease
## Primary_biliary_cirrhosis
## Systemic_lupus_erythematosus
## Psoriasis
##
## Cluster02 has 14 members
## Type_2_diabetes
## Fasting_glucose_related_traits
## Red_blood_cell_traits
## Crohns_disease
## Migraine
## Systemic_sclerosis
## Ankylosing_spondylitis
## Platelet_counts
## Triglycerides
## HDL_cholesterol
## Vitiligo
## Progressive_supranuclear_palsy
## Liver_enzyme_levels_gamma_glutamyl_transferase
## LDL_cholesterol
##
## Cluster03 has 11 members
## Allergy
## Type_1_diabetes
## Primary_sclerosing_cholangitis
## Juvenile_idiopathic_arthritis
## Behcets_disease
## Ulcerative_colitis
## Rheumatoid_arthritis
## Autoimmune_thyroiditis
## Alopecia_areata
## C_reactive_protein
## Asthma
##
## Cluster04 has 8 members
## Bone_mineral_density
## Chronic_kidney_disease
## Alzheimers_combined
## Restless_legs_syndrome
## Atopic_dermatitis
## Urate_levels
## Renal_function_related_traits_BUN
## Creatinine_levels
## The “Enrichment 1/2” columns show the average p-values of the group-specific SNPs-regulatory associations. A “-” sign indicates that an association is underrepresented. The “p-value” column shows whether the difference in the associations bwtween the groups is statistically significantly different.
## [1] "c1 vs. c2 , number of degs significant at adj.p.val<0.5: 58"
##
## -------------------------------------------------------------------------------------------------------------
## Row.names V2 c1 c2 adj.P.Val
## --------------------------------------------------- ----------------------------- ------- ------- -----------
## wgEncodeUwHistoneHuvecH3k27me3StdHotspotsRep1 HUVEC H3K27me3 Histone Mod -0.9549 -0.8483 0.9989
## ChIP-seq Hotspots 1 from
## ENCODE/UW
##
## wgEncodeBroadHistoneHsmmtH2azStdPk HSMMtube H2A.Z Histone Mods 0.6133 0.533 0.9989
## by ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeUwHistoneNhekH3k4me3StdHotspotsRep1 NHEK H3K4me3 Histone Mod 0.7822 0.8106 0.9989
## ChIP-seq Hotspots 1 from
## ENCODE/UW
##
## wgEncodeUwHistoneHmecH3k27me3StdPkRep1 HMEC H3K27me3 Histone Mod 1 0.9834 0.9989
## ChIP-seq Peaks 1 from
## ENCODE/UW
##
## wgEncodeBroadHistoneK562Chd4mi2Pk K562 CHD4 Mi2 Histone Mods by 0.05905 0.07032 0.9989
## ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeUwHistoneH7esH3k27me3StdDiffa2dHotspotsRep2 H7-hESC H3K27me3 diffProtA 2 -0.732 -0.82 0.9989
## d Histone Mod ChIP-seq
## Hotspots 2 from ENCODE/UW
##
## wgEncodeUwHistoneNhekH3k27me3StdPkRep2 NHEK H3K27me3 Histone Mod 1 0.9759 0.9989
## ChIP-seq Peaks 2 from
## ENCODE/UW
##
## wgEncodeUwHistoneHepg2H3k4me3StdPkRep1 HepG2 H3K4me3 Histone Mod 0.7085 0.6941 0.9989
## ChIP-seq Peaks 1 from
## ENCODE/UW
##
## wgEncodeUwHistoneRptecH3k04me3StdHotspotsRep1 RPTEC H3K4me3 Histone Mod 0.5804 0.6006 0.9989
## ChIP-seq Hotspots 1 from
## ENCODE/UW
##
## wgEncodeUwHistoneWi38H3k04me3OhtamStdPkRep2 WI-38 H3K4me3 4-OHTAM 20 nM 0.9424 0.9167 0.9989
## 72 hr Histone Mod ChIP-seq
## Peaks 2 from ENCODE/UW
## -------------------------------------------------------------------------------------------------------------
##
## [1] "c1 vs. c3 , number of degs significant at adj.p.val<0.5: 57"
##
## -------------------------------------------------------------------------------------------------------
## Row.names V2 c1 c3 adj.P.Val
## --------------------------------------------- ----------------------------- ------- ------- -----------
## wgEncodeUwHistoneNhekH3k27me3StdPkRep2 NHEK H3K27me3 Histone Mod 1 1 1
## ChIP-seq Peaks 2 from
## ENCODE/UW
##
## wgEncodeUwHistoneH7esH3k04me3StdDiffa5dPkRep1 H7-hESC H3K4me3 diffProtA 5 d 0.9222 0.9253 0.9941
## Histone Mod ChIP-seq Peaks 1
## from ENCODE/UW
##
## wgEncodeUwHistoneNhekH3k4me3StdHotspotsRep1 NHEK H3K4me3 Histone Mod 0.7822 0.7747 0.9939
## ChIP-seq Hotspots 1 from
## ENCODE/UW
##
## wgEncodeBroadHistoneK562H4k20me1StdPk K562 H4K20me1 Histone Mods by -0.4484 -0.4256 0.9939
## ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeUwHistoneAg04450H3k27me3StdPkRep1 AG04450 H3K27me3 Histone Mod 0.9824 0.9768 0.9939
## ChIP-seq Peaks 1 from
## ENCODE/UW
##
## wgEncodeSydhHistoneHct116H3k04me1UcdPk HCT-116 H3K4me1 Histone -0.8711 -0.9098 0.9936
## Modifications by ChIP-seq
## Peaks from ENCODE/SYDH
##
## wgEncodeUwHistoneWi38H3k04me3OhtamStdPkRep2 WI-38 H3K4me3 4-OHTAM 20 nM 0.9424 0.9231 0.9936
## 72 hr Histone Mod ChIP-seq
## Peaks 2 from ENCODE/UW
##
## wgEncodeBroadHistoneDnd41H3k09me3Pk Dnd41 H3K9me3 Histone Mods by 0.5799 0.5264 0.9936
## ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeUwHistoneWi38H3k04me3StdPkRep1 WI-38 H3K4me3 Histone Mod 0.9007 0.8748 0.9936
## ChIP-seq Peaks 1 from
## ENCODE/UW
##
## wgEncodeSydhHistonePanc1H3k27acUcdPk PANC-1 H3K27ac Histone 0.7276 0.7498 0.9936
## Modifications by ChIP-Seq
## Peaks from ENCODE/SYDH
## -------------------------------------------------------------------------------------------------------
##
## [1] "c1 vs. c4 , number of degs significant at adj.p.val<0.5: 74"
##
## -----------------------------------------------------------------------------------------------------
## Row.names V2 c1 c4 adj.P.Val
## ----------------------------------------- ----------------------------- -------- -------- -----------
## wgEncodeBroadHistoneH1hescSuz12051317Pk H1-hESC SUZ12 (05-1317) -0.779 -0.7865 0.9972
## Histone Mods by ChIP-seq
## Peaks from ENCODE/Broad
##
## wgEncodeBroadHistoneH1hescSirt6Pk H1-hESC SIRT6 Histone Mods by -0.114 -0.1162 0.9972
## ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeBroadHistoneNhekH4k20me1StdPk NHEK H4K20me1 Histone Mods by -0.05739 -0.05835 0.9972
## ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeBroadHistoneNhdfadH3k27me3StdPk NHDF-Ad H3K27me3 Histone Mods -0.07535 -0.08736 0.9962
## by ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeBroadHistoneH1hescHdac6a301341aPk H1-hESC HDAC6 (A301-341A) -0.4709 -0.4481 0.9962
## Histone Mods by ChIP-seq
## Peaks from ENCODE/Broad
##
## wgEncodeBroadHistoneK562CtcfStdPk K562 CTCF Histone Mods by 0.8517 0.8325 0.9962
## ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeBroadHistoneHuvecH3k27me3StdPk HUVEC H3K27me3 Histone Mods 0.399 0.4299 0.9962
## by ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeBroadHistoneOsteoH3k27me3Pk Osteoblasts H3K27me3 Histone -0.1248 -0.1426 0.9962
## Mods by ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeBroadHistoneK562PcafPk K562 PCAF Histone Mods by -0.5469 -0.5158 0.9962
## ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeBroadHistoneNhdfadCtcfStdPk NHDF-Ad CTCF Histone Mods by 0.5762 0.5656 0.9962
## ChIP-seq Peaks from
## ENCODE/Broad
## -----------------------------------------------------------------------------------------------------
##
## [1] "c2 vs. c3 , number of degs significant at adj.p.val<0.5: 41"
##
## --------------------------------------------------------------------------------------------------------
## Row.names V2 c2 c3 adj.P.Val
## ---------------------------------------------- ----------------------------- ------- ------- -----------
## wgEncodeUwHistoneHcfaaH3k4me3StdHotspotsRep1 HCFaa H3K4me3 Histone Mod 0.9004 -0.8929 0.9986
## ChIP-seq Hotspots 1 from
## ENCODE/UW
##
## wgEncodeUwHistoneHmfH3k4me3StdHotspotsRep2 HMF H3K4me3 Histone Mod 0.8024 0.7632 0.9986
## ChIP-seq Hotspots 2 from
## ENCODE/UW
##
## wgEncodeUwHistoneNhdfneoH3k4me3StdHotspotsRep1 NHDF-neo H3K4me3 Histone Mod 0.7696 0.9301 0.9986
## ChIP-seq Hotspots 1 from
## ENCODE/UW
##
## wgEncodeUwHistoneNhlfH3k04me3StdHotspotsRep1 NHLF H3K4me3 Histone Mod 0.9589 0.8002 0.9986
## ChIP-seq Hotspots 1 from
## ENCODE/UW
##
## wgEncodeUwHistoneBjH3k4me3StdPkRep1 BJ H3K4me3 Histone Mod 0.9244 0.9502 0.9986
## ChIP-seq Peaks 1 from
## ENCODE/UW
##
## wgEncodeUwHistoneNhekH3k4me3StdHotspotsRep1 NHEK H3K4me3 Histone Mod 0.8106 0.7747 0.9986
## ChIP-seq Hotspots 1 from
## ENCODE/UW
##
## wgEncodeUwHistoneH7esH3k4me3StdPkRep2 H7-hESC H3K4me3 Histone Mod 0.9491 0.9732 0.9986
## ChIP-seq Peaks 2 from
## ENCODE/UW
##
## wgEncodeBroadHistoneDnd41H3k04me1Pk Dnd41 H3K4me1 Histone Mods by -0.6213 -0.7878 0.9986
## ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeUwHistoneHmecH3k27me3StdPkRep1 HMEC H3K27me3 Histone Mod 0.9834 0.9629 0.9986
## ChIP-seq Peaks 1 from
## ENCODE/UW
##
## wgEncodeBroadHistoneMonocd14ro1746H3k04me2Pk Monocytes CD14+ H3K4me2 0.1098 0.1309 0.9986
## Histone Mods by ChIP-seq
## Peaks from ENCODE/Broad
## --------------------------------------------------------------------------------------------------------
##
## [1] "c2 vs. c4 , number of degs significant at adj.p.val<0.5: 9"
##
## --------------------------------------------------------------------------------------------------------
## Row.names V2 c2 c4 adj.P.Val
## -------------------------------------------- ----------------------------- -------- -------- -----------
## wgEncodeBroadHistoneHelas3Ezh239875Pk HeLa-S3 EZH2 (39875) Histone 0.6315 0.6288 0.9989
## Mods by ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeUwHistoneHmecH3k4me3StdHotspotsRep2 HMEC H3K4me3 Histone Mod 0.7418 0.7364 0.9974
## ChIP-seq Hotspots 2 from
## ENCODE/UW
##
## wgEncodeUwHistoneHcmH3k4me3StdPkRep2 HCM H3K4me3 Histone Mod 0.91 0.906 0.9974
## ChIP-seq Peaks 2 from
## ENCODE/UW
##
## wgEncodeUwHistoneHbmecH3k4me3StdHotspotsRep1 HBMEC H3K4me3 Histone Mod 0.7582 0.7546 0.9974
## ChIP-seq Hotspots 1 from
## ENCODE/UW
##
## wgEncodeBroadHistoneHsmmH3k27me3StdPk HSMM H3K27me3 Histone Mods by -0.02327 -0.02171 0.9974
## ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeBroadHistoneHelas3H3k27me3StdPk HeLa-S3 H3K27me3 Histone Mods -0.3401 -0.3264 0.9974
## by ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeUwHistoneAg04449H3k4me3StdPkRep2 AG04449 H3K4me3 Histone Mod 0.9604 0.9619 0.9974
## ChIP-seq Peaks 2 from
## ENCODE/UW
##
## wgEncodeUwHistoneHmfH3k4me3StdHotspotsRep1 HMF H3K4me3 Histone Mod 0.8905 0.8934 0.9974
## ChIP-seq Hotspots 1 from
## ENCODE/UW
##
## wgEncodeBroadHistoneMonocd14ro1746H2azPk Monocytes CD14+ H2A.Z Histone -0.5731 -0.5801 0.9974
## Mods by ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeUwHistoneCaco2H3k36me3StdPkRep1 Caco-2 H3K36me3 Histone Mod 0.9984 1 0.9974
## ChIP-seq Peaks 1 from
## ENCODE/UW
## --------------------------------------------------------------------------------------------------------
##
## [1] "c3 vs. c4 , number of degs significant at adj.p.val<0.5: 0"
##
## -------------------------------------------------------------------------------------------------------
## Row.names V2 c3 c4 adj.P.Val
## --------------------------------------------- ----------------------------- ------- ------- -----------
## wgEncodeBroadHistoneHsmmtEzh239875Pk HSMMtube EZH2 (39875) Histone 0.5422 0.5409 0.9993
## Mods by ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeBroadHistoneHuvecCtcfStdPk HUVEC CTCF Histone Mods by 0.8847 0.8878 0.9993
## ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeUwHistoneGm12878H3k27me3StdPkRep2 GM12878 H3K27me3 Histone Mod 0.8888 0.8864 0.9952
## ChIP-seq Peaks 2 from
## ENCODE/UW
##
## wgEncodeBroadHistoneHsmmtCtcfStdPk HSMMtube CTCF Histone Mods by -0.9344 -0.9554 0.9952
## ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeBroadHistoneK562Ezh239875StdPk K562 EZH2 (39875) Histone 0.154 0.1636 0.9935
## Mods by ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeBroadHistoneHuvecH3k9acStdPk HUVEC H3K9ac Histone Mods by 0.8172 0.8315 0.9935
## ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeUwHistoneK562H3k36me3StdPkRep1 K562 H3K36me3 Histone Mod 0.9909 1 0.9885
## ChIP-seq Peaks 1 from
## ENCODE/UW
##
## wgEncodeUwHistoneH7esH3k4me3StdPkRep1 H7-hESC H3K4me3 Histone Mod 0.8372 0.8307 0.9878
## ChIP-seq Peaks 1 from
## ENCODE/UW
##
## wgEncodeUwHistoneCaco2H3k36me3StdHotspotsRep2 Caco-2 H3K36me3 Histone Mod -0.981 -0.9489 0.9831
## ChIP-seq Hotspots 2 from
## ENCODE/UW
##
## wgEncodeBroadHistoneK562Rnf2Pk K562 RNF2 Histone Mods by 0.02664 0.02957 0.9831
## ChIP-seq Peaks from
## ENCODE/Broad
## -------------------------------------------------------------------------------------------------------Text mining question 2: Are the terms associated stronger with the diseases in one vs. the other cluster based on the literature strength? Are the terms themselves related based on the literature? Expected answer: Yes, the literature associations should confirm the relationships.
Summary
- Again, cluster 1 is strongly distinct. Cluster 2 is less so. Histone marks seem all active.
| C1 | C2 | C3 | C4 | |
|---|---|---|---|---|
| C1 | Cell types: Gm12878, CD20+ Reg: H3K4me1, H3K9me3, H3K9ac, H3K27ac, H2az, H3K4me2 | Cell types: Gm12878, CD20+ Reg: H3K4me1, H3K9me3, H3K9ac, H3K27ac, H2az, H3K4me2 | Cell types: Gm12878, CD20+ Reg: H3K4me1, H3K9me3, H3K9ac, H3K27ac, H2az, H3K4me2 | |
| C2 | Cell types: K562, NHEK, NHDF-Ad, NH-A, HMEC Reg: H3K36me3, H4K20me1, H3K79me2 | Nothing significant | ||
| C3 | Nothing significant | |||
| C4 |
Analysis of all regulatory datasets
Out of all regulatory datasets, we select all. The goal here is to get potentially tighter clustering.
## [1] 4498 39## [1] 2969 39
The top 10 pairs of disease-associated SNPs are most similar with each other.
##
## --------------------------------------------------------------------------------------------
## Disease 1 Disease 2 Corr. coefficient
## ---------------------------------------------- ------------------------- -------------------
## HDL_cholesterol Triglycerides 0.473
##
## LDL_cholesterol Triglycerides 0.4314
##
## Chronic_kidney_disease Urate_levels 0.3742
##
## HDL_cholesterol LDL_cholesterol 0.3475
##
## Bone_mineral_density Type_2_diabetes 0.3225
##
## Multiple_sclerosis Primary_biliary_cirrhosis 0.316
##
## Alzheimers_combined Type_2_diabetes 0.2999
##
## Liver_enzyme_levels_gamma_glutamyl_transferase Urate_levels 0.2976
##
## Fasting_glucose_related_traits Type_2_diabetes 0.2972
##
## Liver_enzyme_levels_gamma_glutamyl_transferase Platelet_counts 0.2944
## --------------------------------------------------------------------------------------------The similarity dendrogram can be divided into separate groups:
## Cluster01 has 6 members
## Platelet_counts
## Liver_enzyme_levels_gamma_glutamyl_transferase
## Red_blood_cell_traits
## LDL_cholesterol
## HDL_cholesterol
## Triglycerides
##
## Cluster02 has 8 members
## Type_2_diabetes
## Fasting_glucose_related_traits
## Bone_mineral_density
## Alzheimers_combined
## Creatinine_levels
## Renal_function_related_traits_BUN
## Urate_levels
## Chronic_kidney_disease
##
## Cluster03 has 9 members
## Multiple_sclerosis
## Kawasaki_disease
## Celiac_disease
## Systemic_lupus_erythematosus
## Psoriasis
## Ulcerative_colitis
## Rheumatoid_arthritis
## Crohns_disease
## Autoimmune_thyroiditis
##
## Cluster04 has 5 members
## Primary_biliary_cirrhosis
## Ankylosing_spondylitis
## Systemic_sclerosis
## Migraine
## Primary_sclerosing_cholangitis
##
## Cluster05 has 11 members
## Juvenile_idiopathic_arthritis
## Atopic_dermatitis
## Alopecia_areata
## C_reactive_protein
## Allergy
## Type_1_diabetes
## Vitiligo
## Behcets_disease
## Progressive_supranuclear_palsy
## Restless_legs_syndrome
## Asthma
## The “Enrichment 1/2” columns show the average p-values of the group-specific SNPs-regulatory associations. A “-” sign indicates that an association is underrepresented. The “p-value” column shows whether the difference in the associations bwtween the groups is statistically significantly different.
## [1] "c1 vs. c2 , number of degs significant at adj.p.val<0.5: 0"
## [1] "c1 vs. c3 , number of degs significant at adj.p.val<0.5: 96"
##
## ------------------------------------------------------------------------------------------------------------------
## Row.names V2 c1 c3 adj.P.Val
## --------------------------------------------------- ----------------------------- ---------- --------- -----------
## wgEncodeHaibTfbsGm12878Foxm1sc502V0422111PkRep1 GM12878 FOXM1 v042211.1 -0.1511 0.002657 0.001287
## ChIP-seq Peaks Rep 1 from
## ENCODE/HAIB
##
## wgEncodeHaibTfbsGm12878Nficsc81335V0422111PkRep1 GM12878 NFIC v042211.1 -0.07057 0.0001995 0.001287
## ChIP-seq Peaks Rep 1 from
## ENCODE/HAIB
##
## wgEncodeOpenChromFaireGm12892Pk GM12892 FAIRE Peaks from -0.1562 0.001429 0.001287
## ENCODE/OpenChrom(UNC)
##
## wgEncodeHaibTfbsGm12878Runx3sc101553V0422111PkRep2 GM12878 RUNX3 v042211.1 -0.2168 0.00165 0.001287
## ChIP-seq Peaks Rep 2 from
## ENCODE/HAIB
##
## wgEncodeUwDnaseGm06990HotspotsRep2 GM06990 DNaseI HS HotSpots -0.1694 0.01795 0.00263
## Rep 2 from ENCODE/UW
##
## wgEncodeHaibTfbsGm12878Cebpbsc150V0422111PkRep1 GM12878 CEBPB v042211.1 -0.4632 0.0321 0.00263
## ChIP-seq Peaks Rep 1 from
## ENCODE/HAIB
##
## wgEncodeHaibTfbsGm12878Nficsc81335V0422111PkRep2 GM12878 NFIC v042211.1 -0.1831 0.02489 0.00263
## ChIP-seq Peaks Rep 2 from
## ENCODE/HAIB
##
## wgEncodeBroadHistoneGm12878H3k9me3StdPk GM12878 H3K9me3 Histone Mods -7.375e-07 7.237e-08 0.00263
## by ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeAwgTfbsSydhGm15510NfkbTnfaIggrabUniPk GM15510 (TNFa) TFBS Uniform -0.6278 0.1354 0.00263
## Peaks of NFKB from
## ENCODE/Stanford/Analysis
##
## wgEncodeUwDnaseTregwb83319432PkRep1 Treg Wb83319432 DNaseI HS -0.4653 0.1548 0.002646
## Peaks Rep 1 from ENCODE/UW
##
## wgEncodeOpenChromDnaseGcbcellPk GC B cell DNaseI HS Peaks -0.4816 0.01565 0.002763
## from ENCODE/Duke
##
## wgEncodeHaibTfbsGm12878Atf2sc81188V0422111PkRep1 GM12878 ATF2 v042211.1 -0.2395 0.002065 0.003196
## ChIP-seq Peaks Rep 1 from
## ENCODE/HAIB
##
## wgEncodeUwHistoneH7esH3k36me3StdDiffa5dHotspotsRep1 H7-hESC H3K36me3 diffProtA 5 0.01797 -0.6381 0.003411
## d Histone Mod ChIP-seq
## Hotspots 1 from ENCODE/UW
##
## wgEncodeUwDnaseCd20ro01778HotspotsRep1 B cells CD20+ RO01778 DNaseI -0.6139 0.0128 0.003411
## HS HotSpots Rep 1 from
## ENCODE/UW
##
## wgEncodeHaibTfbsGm12878Pmlsc71910V0422111PkRep2 GM12878 PML v042211.1 -0.3213 0.0004603 0.003411
## ChIP-seq Peaks Rep 2 from
## ENCODE/HAIB
##
## wgEncodeHaibTfbsGm12878Atf2sc81188V0422111PkRep2 GM12878 ATF2 v042211.1 -0.283 0.007315 0.003411
## ChIP-seq Peaks Rep 2 from
## ENCODE/HAIB
##
## wgEncodeHaibTfbsGm12878Stat5asc74442V0422111PkRep2 GM12878 STAT5A v042211.1 -0.3552 0.001387 0.003411
## ChIP-seq Peaks Rep 2 from
## ENCODE/HAIB
##
## wgEncodeHaibTfbsHepg2P300V0416101PkRep2 HepG2 p300 v041610.1 ChIP-seq 0.01642 -0.8081 0.003411
## Peaks Rep 2 from ENCODE/HAIB
##
## wgEncodeHaibTfbsGm12878Stat5asc74442V0422111PkRep1 GM12878 STAT5A v042211.1 -0.3271 0.007786 0.003411
## ChIP-seq Peaks Rep 1 from
## ENCODE/HAIB
##
## wgEncodeGisRnaPetNhekNucleusPapClustersRep1 NHEK nucleus polyA+ 0.0004188 -0.0943 0.003411
## clone-free RNA PET Clusters
## Rep 1 from ENCODE/GIS
## ------------------------------------------------------------------------------------------------------------------
##
## [1] "c1 vs. c4 , number of degs significant at adj.p.val<0.5: 0"
## [1] "c1 vs. c5 , number of degs significant at adj.p.val<0.5: 50"
##
## ----------------------------------------------------------------------------------------------------------------
## Row.names V2 c1 c5 adj.P.Val
## --------------------------------------------------- ----------------------------- --------- -------- -----------
## wgEncodeUwHistoneH7esH3k36me3StdDiffa5dHotspotsRep1 H7-hESC H3K36me3 diffProtA 5 0.01797 -0.3008 0.001831
## d Histone Mod ChIP-seq
## Hotspots 1 from ENCODE/UW
##
## wgEncodeBroadHistoneA549H3k36me3Etoh02Pk A549 EtOH 0.02% H3K36me3 9.345e-05 -0.04379 0.01678
## Histone Mods by ChIP-seq
## Peaks from ENCODE/Broad
##
## wgEncodeBroadHistoneHuvecH3k79me2Pk HUVEC H3K79me2 Histone Mods 0.0001253 -0.0382 0.01678
## by ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeHaibTfbsHepg2P300V0416101PkRep2 HepG2 p300 v041610.1 ChIP-seq 0.01642 0.9518 0.02286
## Peaks Rep 2 from ENCODE/HAIB
##
## wgEncodeBroadHistoneNhekH3k79me2Pk NHEK H3K79me2 Histone Mods by 9.553e-05 -0.05467 0.02298
## ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeUwHistoneH7esH3k36me3StdDiffa2dHotspotsRep2 H7-hESC H3K36me3 diffProtA 2 0.04253 -0.4979 0.02655
## d Histone Mod ChIP-seq
## Hotspots 2 from ENCODE/UW
##
## wgEncodeUwHistoneH7esH3k36me3StdDiffa9dHotspotsRep2 H7-hESC H3K36me3 diffProtA 9 0.2216 -0.813 0.02655
## d Histone Mod ChIP-seq
## Hotspots 2 from ENCODE/UW
##
## wgEncodeHaibTfbsHepg2Foxa1sc6553V0416101PkRep2 HepG2 FOXA1 6553 v041610.1 0.1367 -0.9871 0.02655
## ChIP-seq Peaks Rep 2 from
## ENCODE/HAIB
##
## wgEncodeHaibTfbsK562Pol2V0416101PkRep2 K562 Pol2 v041610.1 ChIP-seq 0.06284 -0.8502 0.02655
## Peaks Rep 2 from ENCODE/HAIB
##
## wgEncodeHaibTfbsHepg2RxraPcr1xPkRep2 HepG2 RXRA PCR1x ChIP-seq 0.1516 0.9869 0.02655
## Peaks Rep 2 from ENCODE/HAIB
##
## wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101PkRep1 HepG2 FOXA2 v041610.1 0.1786 -0.9735 0.02655
## ChIP-seq Peaks Rep 1 from
## ENCODE/HAIB
##
## wgEncodeBroadHistoneOsteoH3k79me2Pk Osteoblasts H3K79me2 Histone 0.001015 -0.063 0.02655
## Mods by ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeBroadHistoneK562H3k36me3StdPk K562 H3K36me3 Histone Mods by 9.543e-07 -0.06262 0.02655
## ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeUwHistoneH7esH3k36me3StdDiffa5dHotspotsRep2 H7-hESC H3K36me3 diffProtA 5 0.01215 -0.5665 0.02655
## d Histone Mod ChIP-seq
## Hotspots 2 from ENCODE/UW
##
## wgEncodeBroadHistoneHepg2H3k04me1StdPk HepG2 H3K4me1 Histone Mods by 0.0001503 -0.1153 0.02655
## ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeBroadHistoneK562Plu1StdPk K562 PLU1 Histone Mods by 0.002636 -0.3623 0.02655
## ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeBroadHistoneA549H3k79me2Dex100nmPk A549 DEX 100 nM H3K79me2 0.0005856 -0.03396 0.02768
## Histone Mods by ChIP-seq
## Peaks from ENCODE/Broad
##
## wgEncodeSydhTfbsK562Pol2Ifng30StdPk K562 Pol2 Standard IFNg 30min 0.01416 0.5688 0.02797
## ChIP-seq Peaks from
## ENCODE/SYDH
##
## wgEncodeBroadHistoneK562H3k4me2StdPk K562 H3K4me2 Histone Mods by 0.0003089 -0.3264 0.03235
## ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeBroadHistoneK562Nsd2ab75359Pk K562 NSD2 (ab75359) Histone 4.581e-06 -0.03612 0.03358
## Mods by ChIP-seq Peaks from
## ENCODE/Broad
## ----------------------------------------------------------------------------------------------------------------
##
## [1] "c2 vs. c3 , number of degs significant at adj.p.val<0.5: 1"
##
## ---------------------------------------------------------------------------------------------
## Row.names V2 c2 c3 adj.P.Val
## -------------------------------------- ---------------------------- ------ ------ -----------
## wgEncodeUwDnaseCd20ro01778HotspotsRep1 B cells CD20+ RO01778 DNaseI -0.204 0.0128 0.0001871
## HS HotSpots Rep 1 from
## ENCODE/UW
## ---------------------------------------------------------------------------------------------
##
## [1] "c2 vs. c4 , number of degs significant at adj.p.val<0.5: 0"
## [1] "c2 vs. c5 , number of degs significant at adj.p.val<0.5: 0"
## [1] "c3 vs. c4 , number of degs significant at adj.p.val<0.5: 0"
## [1] "c3 vs. c5 , number of degs significant at adj.p.val<0.5: 121"
##
## --------------------------------------------------------------------------------------------------------------
## Row.names V2 c3 c5 adj.P.Val
## -------------------------------------------------- ----------------------------- --------- ------- -----------
## wgEncodeUwDnaseCd20ro01778HotspotsRep1 B cells CD20+ RO01778 DNaseI 0.0128 -0.8139 0.006385
## HS HotSpots Rep 1 from
## ENCODE/UW
##
## wgEncodeHaibTfbsGm12878Runx3sc101553V0422111PkRep2 GM12878 RUNX3 v042211.1 0.00165 0.8762 0.006385
## ChIP-seq Peaks Rep 2 from
## ENCODE/HAIB
##
## wgEncodeSydhTfbsGm12878Stat1StdPk GM12878 STAT1 Standard 0.0506 0.9299 0.006385
## ChIP-seq Peaks from
## ENCODE/SYDH
##
## wgEncodeOpenChromFaireGm12892Pk GM12892 FAIRE Peaks from 0.001429 0.8088 0.006385
## ENCODE/OpenChrom(UNC)
##
## wgEncodeHaibTfbsGm12878Nficsc81335V0422111PkRep1 GM12878 NFIC v042211.1 0.0001995 0.8082 0.006385
## ChIP-seq Peaks Rep 1 from
## ENCODE/HAIB
##
## wgEncodeHaibTfbsGm12878Foxm1sc502V0422111PkRep1 GM12878 FOXM1 v042211.1 0.002657 0.8098 0.006385
## ChIP-seq Peaks Rep 1 from
## ENCODE/HAIB
##
## wgEncodeHaibTfbsGm12878Bclaf101388V0416101PkRep2 GM12878 BCLAF1 v041610.1 0.01372 -0.9888 0.006385
## ChIP-seq Peaks Rep 2 from
## ENCODE/HAIB
##
## wgEncodeOpenChromDnaseGcbcellPk GC B cell DNaseI HS Peaks 0.01565 0.8617 0.006385
## from ENCODE/Duke
##
## wgEncodeHaibTfbsGm12878Cebpbsc150V0422111PkRep1 GM12878 CEBPB v042211.1 0.0321 0.8974 0.006385
## ChIP-seq Peaks Rep 1 from
## ENCODE/HAIB
##
## wgEncodeHaibTfbsGm12878Pmlsc71910V0422111PkRep2 GM12878 PML v042211.1 0.0004603 0.8089 0.006385
## ChIP-seq Peaks Rep 2 from
## ENCODE/HAIB
##
## wgEncodeAwgTfbsHaibGm12878Bcl3V0416101UniPk GM12878 TFBS Uniform Peaks of 0.192 0.9753 0.007999
## BCL3 from
## ENCODE/HudsonAlpha/Analysis
##
## wgEncodeHaibTfbsGm12878Mta3sc81325V0422111PkRep2 GM12878 MTA3 v042211.1 6.729e-05 -0.9847 0.008267
## ChIP-seq Peaks Rep 2 from
## ENCODE/HAIB
##
## wgEncodeHaibTfbsGm12878Stat5asc74442V0422111PkRep1 GM12878 STAT5A v042211.1 0.007786 -0.9993 0.008703
## ChIP-seq Peaks Rep 1 from
## ENCODE/HAIB
##
## wgEncodeHaibTfbsGm12878Stat5asc74442V0422111PkRep2 GM12878 STAT5A v042211.1 0.001387 0.6498 0.008703
## ChIP-seq Peaks Rep 2 from
## ENCODE/HAIB
##
## wgEncodeAwgTfbsSydhGm19193NfkbTnfaIggrabUniPk GM19193 (TNFa) TFBS Uniform 0.2949 0.9464 0.008703
## Peaks of NFKB from
## ENCODE/Stanford/Analysis
##
## wgEncodeAwgTfbsSydhGm15510NfkbTnfaIggrabUniPk GM15510 (TNFa) TFBS Uniform 0.1354 0.8731 0.008703
## Peaks of NFKB from
## ENCODE/Stanford/Analysis
##
## wgEncodeHaibTfbsGm12878Atf2sc81188V0422111PkRep1 GM12878 ATF2 v042211.1 0.002065 0.7675 0.008703
## ChIP-seq Peaks Rep 1 from
## ENCODE/HAIB
##
## wgEncodeHaibTfbsGm12878Taf1Pcr1xPkRep2 GM12878 TAF1 PCR1x ChIP-seq 0.07538 0.8878 0.009775
## Peaks Rep 2 from ENCODE/HAIB
##
## wgEncodeSydhTfbsGm12878Corestsc30189IggmusPk GM12878 COREST SC30189 0.0202 0.839 0.009905
## IgG-mus ChIP-seq Peaks from
## ENCODE/SYDH
##
## wgEncodeHaibTfbsGm12891Pol2Pcr1xPkRep1 GM12891 Pol2 PCR1x ChIP-seq 0.03033 0.9942 0.009905
## Peaks Rep 1 from ENCODE/HAIB
## --------------------------------------------------------------------------------------------------------------
##
## [1] "c4 vs. c5 , number of degs significant at adj.p.val<0.5: 0"## [1] "Counts of regulatory elements differentially associated with each group"##
## ---------------------------------
## c1 c2 c3 c4 c5
## -------- ---- ---- ---- ---- ----
## **c1** 0 0 96 0 50
##
## **c2** 0 0 1 0 0
##
## **c3** 0 0 0 0 121
##
## **c4** 0 0 0 0 0
##
## **c5** 0 0 0 0 0
## ---------------------------------Summary
The picture is not as good as when we are taking subsets of regulatory datasets.
Overlap analysis
## Using V3 as value column: use value.var to override.